She didn't say she didn't respect him as a person, just not as a man.

When she had been much much younger Fujiko would probably have told him that she'll do what she wants. More than anything she hated being controlled back then. She was no longer that girl, however (and she knew that she would have regretted it after even back then).

Instead, she huffs and leans down to press her forehead against his if he'd let her.

"Fujiko will promise only if you promise to actually talk to me when you have a problem."